User: doctor.dee005

gravatar for doctor.dee005
doctor.dee005170
Reputation:
170
Status:
Trusted
Location:
Bioinformatics Center, Pune
Last seen:
1 day, 13 hours ago
Joined:
2 years, 1 month ago
Email:
d************@gmail.com

Posts by doctor.dee005

<prev • 51 results • page 1 of 6 • next >
1
vote
2
answers
145
views
2
answers
Comment: C: Amino Acid matrices freely downloadable url
... See the link [POP][1]. You can also find some references and original scripts to generate the matrix there. [1]: http://www.drive5.com/pop/VTML200I ...
written 5 days ago by doctor.dee005170
3
votes
2
answers
145
views
2
answers
Answer: A: Amino Acid matrices freely downloadable url
... BLOSUM and PAM series matrices are available on NCBI ftp. See this link: ftp://ftp.ncbi.nih.gov/blast/matrices/ ...
written 7 days ago by doctor.dee005170
0
votes
3
answers
2.1k
views
3
answers
Answer: A: How to plot length distribution of contigs in the assembly?
... use this [Python script][1]. Easy to use: python contigPlot.py fastaDir. Where fastaDir is directory name containing genome files (extension .fasta) [1]: https://github.com/drdee255/code-Util/blob/master/contigPlot.py ...
written 7 days ago by doctor.dee005170
0
votes
0
answers
178
views
0
answers
Comment: C: Suggestions for better and accurate tool for PanGenome analysis.
... I have several microbial genomes and protein files from multiple genera. I have tried [BPGA][1] but it cantbe automated. [1]: http://iicb.res.in/bpga/index.html ...
written 8 weeks ago by doctor.dee005170
0
votes
0
answers
178
views
0
answers
Suggestions for better and accurate tool for PanGenome analysis.
... I am doing pan genome analysis of multiple genera. I am searching a tool which will work on protein files (I have annotated proteins for each genome). I wanted to run [Roary][1], but it requires .gff files as well. Any suggestions are welcomed. [1]: https://github.com/sanger-pathogens/Roary/tre ...
genome gene pangenome sequencing written 8 weeks ago by doctor.dee005170
0
votes
1
answer
165
views
1
answers
Answer: A: download genbank sequences with exon sequences highlighted
... You can use efetch from ncbi-entrez-direct utilities. But first, you must have the accessions (with start and end of seuences which you want to extract). Make one file for this data and use following command in any script. efetch -db nuccore -id NG_007524.1 -format fasta -chr_start start -chr_stop ...
written 9 weeks ago by doctor.dee005170
1
vote
2
answers
241
views
2
answers
Answer: A: Programmatically retrieve the length of a gene
... Use [seq_stat.py][1], it will give output as tab-separated file, containg header, count of each nucleotide and sequence length. If multifasta file is provided, it will print this statistics. The sequence length of each sequence will be in last column. [1]: https://github.com/drdee255/Python-code ...
written 9 weeks ago by doctor.dee005170
0
votes
1
answer
122
views
1
answers
Answer: A: Extract Reverse Reads Based on Header Information of Forward Reads
... use [fastq-pair][1], it gives the only reads which are in forward and reverse files. So, rather than making forward.txt(headers), make forward.fastq(containg reads for which you want reverse reads to be extracted) and run the program. This will make four files in the directory: 1. forward.fastq.p ...
written 9 weeks ago by doctor.dee005170
1
vote
1
answer
181
views
1
answers
Answer: A: Continuous mismatch at the end of the alignment, how to eliminate it?
... The trailing unaligned regions are results of global alignments. Use mafft --localpair (local alignment), in which trailing unialign regions from both the ends are not considered in order to maximiza alignment scores. ...
written 10 weeks ago by doctor.dee005170
0
votes
1
answer
140
views
1
answers
Answer: A: Advice for trimming asymmetric adapters for paired end sequencing library
... You can use [trimmomatic][1] for this kind of trimming where you can include your adapters in their adapter library and perform trimming. [1]: http://www.usadellab.org/cms/?page=trimmomatic ...
written 10 weeks ago by doctor.dee005170

Latest awards to doctor.dee005

Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Amino Acid matrices freely downloadable url
Scholar 11 weeks ago, created an answer that has been accepted. For A: Extract specific fasta sequences from multiple multi-fasta files located in a di

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 769 users visited in the last hour